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Chromatin Immunoprecipitation- ChIP02:36

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Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
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CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion
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ChimeraScan: a tool for identifying chimeric transcription in sequencing data.

Matthew K Iyer1, Arul M Chinnaiyan, Christopher A Maher

  • 1Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.

Bioinformatics (Oxford, England)
|August 16, 2011
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Summary

Next generation sequencing (NGS) enables gene fusion discovery in cancer. ChimeraScan is an open-source tool for finding chimeric transcripts in high-throughput sequencing data.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Cancer Research

Background:

  • Next generation sequencing (NGS) technologies facilitate novel gene fusion discovery.
  • Gene fusions are critical in cancer development and hold therapeutic potential.

Purpose of the Study:

  • To introduce ChimeraScan, an open-source software package.
  • To enable the discovery of chimeric transcription between independent transcripts.

Main Methods:

  • Utilized high-throughput transcriptome sequencing data.
  • Developed and applied the ChimeraScan software package.

Main Results:

  • Successfully identified chimeric transcripts.
  • Demonstrated the utility of ChimeraScan for gene fusion discovery.

Conclusions:

  • ChimeraScan facilitates de novo gene fusion discovery using NGS data.
  • Identified gene fusions can serve as therapeutic targets in oncology.